argument "object" is missing, with no default while plotting embeddings

[reyvnth]

cao$plotEmbedding(color.by='cell.groups')

Error in (new("standardGeneric", .Data = function (object, ...) :
argument "object" is missing, with no default

[rrydbirk]

Hi @reyvnth

Thanks for pointing this out. I assume this is related to the latest release of sccore v. 1.0.6 that handles plotting.

@VPetukhov @evanbiederstedt is it something you can look into? Also, please note the difference between not setting and setting color.by.

---

> cao$plotEmbedding()
Error in (new("standardGeneric", .Data = function (object, ...)  : 
  argument "object" is missing, with no default
> traceback()
7: as.data.frame(object)
6: tibble::rownames_to_column(as.data.frame(object), "CellName")
5: .local(object, ...)
4: (new("standardGeneric", .Data = function (object, ...) 
   standardGeneric("embeddingPlot"), generic = structure("embeddingPlot", package = "sccore"), 
       package = "sccore", group = list(), valueClass = character(0), 
       signature = "object", default = NULL, skeleton = (function (object, 
           ...) 
       stop(gettextf("invalid call in method dispatch to '%s' (no default method)", 
           "embeddingPlot"), domain = NA))(object, ...)))(embedding = structure(c(0.611773955976275, 
   -0.201864619499218, 0.866376187520284, 0.990715651735666, -0.236066606766107, 
   1.51129312678633, -0.801510330959348, -1.79761297890964, -1.93450844185601, 
   -0.806349409110103, -1.3112358373234, -1.28778215694177, -1.62374350127455, 
   -1.67684190756348, -2.03274148467198, -0.850874008607331, -1.35506921817021, 
   -0.458448124332866, -1.8577399228881, -0.629197642612193, -2.01091144367372, 
   -1.33422349088667, 0.0788846883838285, -0.63587183491603, -0.902618487725923, 
   0.141860972428638, -1.11020208575338, 0.344414721202607, 0.194384006545413, 
   0.593062507710176, -1.02619476884006, 0.124346916396123, 0.798164943292509, 
   1.41078079342649, 0.531973992258964, 0.98181629985409, 0.787428224207245, 
   1.11445239663833, -1.67173579009613, -2.11074254680943, -2.24529472005912, 
   -2.31215557901355, -1.46786133693516, -1.52967462298464, -1.47832217345066, 
   -2.29147348819915, -1.82752420937963, -2.0849462434727, 1.15016190248311, 
   1.28617219421225, -1.64027871382795, -0.969194508234219, 0.627101535348503, 
    ...
3: (new("standardGeneric", .Data = function (object, ...) 
   standardGeneric("embeddingPlot"), generic = structure("embeddingPlot", package = "sccore"), 
       package = "sccore", group = list(), valueClass = character(0), 
       signature = "object", default = NULL, skeleton = (function (object, 
           ...) 
       stop(gettextf("invalid call in method dispatch to '%s' (no default method)", 
           "embeddingPlot"), domain = NA))(object, ...)))(embedding = structure(c(0.611773955976275, 
   -0.201864619499218, 0.866376187520284, 0.990715651735666, -0.236066606766107, 
   1.51129312678633, -0.801510330959348, -1.79761297890964, -1.93450844185601, 
   -0.806349409110103, -1.3112358373234, -1.28778215694177, -1.62374350127455, 
   -1.67684190756348, -2.03274148467198, -0.850874008607331, -1.35506921817021, 
   -0.458448124332866, -1.8577399228881, -0.629197642612193, -2.01091144367372, 
   -1.33422349088667, 0.0788846883838285, -0.63587183491603, -0.902618487725923, 
   0.141860972428638, -1.11020208575338, 0.344414721202607, 0.194384006545413, 
   0.593062507710176, -1.02619476884006, 0.124346916396123, 0.798164943292509, 
   1.41078079342649, 0.531973992258964, 0.98181629985409, 0.787428224207245, 
   1.11445239663833, -1.67173579009613, -2.11074254680943, -2.24529472005912, 
   -2.31215557901355, -1.46786133693516, -1.52967462298464, -1.47832217345066, 
   -2.29147348819915, -1.82752420937963, -2.0849462434727, 1.15016190248311, 
   1.28617219421225, -1.64027871382795, -0.969194508234219, 0.627101535348503, 
    ...
2: rlang::exec(sccore::embeddingPlot, !!!params)
1: cao$plotEmbedding()
> cao$plotEmbedding(color.by = "cell.groups")
Error in (new("standardGeneric", .Data = function (object, ...)  : 
  argument "object" is missing, with no default
> traceback()
7: as.data.frame(object)
6: tibble::rownames_to_column(as.data.frame(object), "CellName")
5: .local(object, ...)
4: (new("standardGeneric", .Data = function (object, ...) 
   standardGeneric("embeddingPlot"), generic = structure("embeddingPlot", package = "sccore"), 
       package = "sccore", group = list(), valueClass = character(0), 
       signature = "object", default = NULL, skeleton = (function (object, 
           ...) 
       stop(gettextf("invalid call in method dispatch to '%s' (no default method)", 
           "embeddingPlot"), domain = NA))(object, ...)))(groups = structure(c(`Donor_05!!9983!!TTGTTCAGTATCGCGC-1` = 3L, 
   `Donor_05!!C744!!ATTCAGGTCGCGCTGA-1` = 3L, `Donor_05!!C746!!AGGTCTACAACACTAC-1` = 3L, 
   `Donor_20!!C751!!CGATGCGTCGACATTG-1` = 3L, `Donor_20!!C751!!TAACACGGTAGACGTG-1` = 3L, 
   `Donor_20!!C751!!TGTACAGAGCAGGTCA-1` = 3L, `Donor_25_poolA!!C746!!AGATCCACACCCGTAG-1` = 3L, 
   `Donor_25_poolA!!C746!!CAACCAAGTGCCCGTA-1` = 3L, `Donor_25_poolA!!C746!!CGGACACAGCGACTAG-1` = 3L, 
   `Donor_25_poolB!!C748!!GCAACCGCAAACCACT-1` = 3L, `Donor_25_poolB!!C750!!AAGAACAAGCACCGTC-1` = 3L, 
   `Donor_25_poolB!!C750!!CTGAGGCGTAGGTTTC-1` = 3L, `Donor_25_poolB!!C751!!AACGGGACACCCTGAG-1` = 3L, 
   `Donor_25_poolB!!C751!!ATCGTGACACCGTACG-1` = 3L, `Donor_29_poolB!!C750!!ATCGTCCAGGGCAGAG-1` = 3L, 
   `Donor_32!!9972!!GTGACGCAGGTGCAGT-1` = 3L, `Donor_32!!9975!!CGATGGCAGCAGCCCT-1` = 3L, 
   `Donor_32!!C744!!CCGTAGGGTAGCTCGC-1` = 3L, `Donor_32!!C746!!CATCCCACATACCGTA-1` = 3L, 
   `Donor_32!!C746!!CCGAACGGTTATGGTC-1` = 3L, `Donor_32!!C746!!GATTGGTAGCTGACAG-1` = 3L, 
   `Donor_32!!C746!!GGTGGCTAGTAAACAC-1` = 3L, `Donor_38!!C744!!AGATGCTTCGTGCACG-1` = 3L, 
   `Donor_38!!C744!!GGGCCATCAGAGCTAG-1` = 3L, `Donor_38!!C744!!GTATTTCCATGACTAC-1` = 3L, 
   `Donor_38!!C744!!TGGGAAGAGCCTCTGG-1` = 3L, `Donor_38!!C746!!CGAGGCTGTCAAGTTC-1` = 3L, 
    ...
3: (new("standardGeneric", .Data = function (object, ...) 
   standardGeneric("embeddingPlot"), generic = structure("embeddingPlot", package = "sccore"), 
       package = "sccore", group = list(), valueClass = character(0), 
       signature = "object", default = NULL, skeleton = (function (object, 
           ...) 
       stop(gettextf("invalid call in method dispatch to '%s' (no default method)", 
           "embeddingPlot"), domain = NA))(object, ...)))(groups = structure(c(`Donor_05!!9983!!TTGTTCAGTATCGCGC-1` = 3L, 
   `Donor_05!!C744!!ATTCAGGTCGCGCTGA-1` = 3L, `Donor_05!!C746!!AGGTCTACAACACTAC-1` = 3L, 
   `Donor_20!!C751!!CGATGCGTCGACATTG-1` = 3L, `Donor_20!!C751!!TAACACGGTAGACGTG-1` = 3L, 
   `Donor_20!!C751!!TGTACAGAGCAGGTCA-1` = 3L, `Donor_25_poolA!!C746!!AGATCCACACCCGTAG-1` = 3L, 
   `Donor_25_poolA!!C746!!CAACCAAGTGCCCGTA-1` = 3L, `Donor_25_poolA!!C746!!CGGACACAGCGACTAG-1` = 3L, 
   `Donor_25_poolB!!C748!!GCAACCGCAAACCACT-1` = 3L, `Donor_25_poolB!!C750!!AAGAACAAGCACCGTC-1` = 3L, 
   `Donor_25_poolB!!C750!!CTGAGGCGTAGGTTTC-1` = 3L, `Donor_25_poolB!!C751!!AACGGGACACCCTGAG-1` = 3L, 
   `Donor_25_poolB!!C751!!ATCGTGACACCGTACG-1` = 3L, `Donor_29_poolB!!C750!!ATCGTCCAGGGCAGAG-1` = 3L, 
   `Donor_32!!9972!!GTGACGCAGGTGCAGT-1` = 3L, `Donor_32!!9975!!CGATGGCAGCAGCCCT-1` = 3L, 
   `Donor_32!!C744!!CCGTAGGGTAGCTCGC-1` = 3L, `Donor_32!!C746!!CATCCCACATACCGTA-1` = 3L, 
   `Donor_32!!C746!!CCGAACGGTTATGGTC-1` = 3L, `Donor_32!!C746!!GATTGGTAGCTGACAG-1` = 3L, 
   `Donor_32!!C746!!GGTGGCTAGTAAACAC-1` = 3L, `Donor_38!!C744!!AGATGCTTCGTGCACG-1` = 3L, 
   `Donor_38!!C744!!GGGCCATCAGAGCTAG-1` = 3L, `Donor_38!!C744!!GTATTTCCATGACTAC-1` = 3L, 
   `Donor_38!!C744!!TGGGAAGAGCCTCTGG-1` = 3L, `Donor_38!!C746!!CGAGGCTGTCAAGTTC-1` = 3L, 
    ...
2: rlang::exec(sccore::embeddingPlot, !!!params)
1: cao$plotEmbedding(color.by = "cell.groups")

[reyvnth]

Thanks a lot, @rrydbirk ! You were right about the sccore version changes causing that issue.

I tried sccore v1.0.5 and did not face any issue. But, I went ahead and fixed the bug, and updated the package to use sccore v1.0.6. I also updated the package to handle SCT assays (if present) in Seurat objects.

@VPetukhov @evanbiederstedt , Please check out the pull request v0.6.0 update (#57) with the fixes.